Starting phenix.real_space_refine on Fri Aug 22 13:20:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5e_38067/08_2025/8x5e_38067.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5e_38067/08_2025/8x5e_38067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5e_38067/08_2025/8x5e_38067.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5e_38067/08_2025/8x5e_38067.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5e_38067/08_2025/8x5e_38067.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5e_38067/08_2025/8x5e_38067.cif" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 15 5.16 5 C 2178 2.51 5 N 501 2.21 5 O 520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3216 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3134 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 82 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 82 Unusual residues: {'6OU': 6, 'PO4': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'6OU:plan-1': 6, '6OU:plan-2': 6, '6OU:plan-3': 6} Unresolved non-hydrogen planarities: 54 Time building chain proxies: 0.96, per 1000 atoms: 0.30 Number of scatterers: 3216 At special positions: 0 Unit cell: (60.35, 75.65, 74.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 15 16.00 P 2 15.00 O 520 8.00 N 501 7.00 C 2178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 72.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.597A pdb=" N ILE A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 296 removed outlier: 4.028A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 345 through 361 removed outlier: 4.179A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.856A pdb=" N TRP A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.598A pdb=" N ALA A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 removed outlier: 3.511A pdb=" N SER A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 5.573A pdb=" N GLU A 436 " --> pdb=" O ASN A 433 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N SER A 437 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 439 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS A 440 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Proline residue: A 455 - end of helix removed outlier: 3.839A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 502 removed outlier: 3.801A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 3.629A pdb=" N PHE A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 512 " --> pdb=" O MET A 508 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 removed outlier: 4.454A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.860A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 Proline residue: A 598 - end of helix removed outlier: 3.919A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.33 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 913 1.34 - 1.45: 770 1.45 - 1.57: 1609 1.57 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3312 Sorted by residual: bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C16 6OU A 707 " pdb=" O18 6OU A 707 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C16 6OU A 705 " pdb=" O18 6OU A 705 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C16 6OU A 706 " pdb=" O18 6OU A 706 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C16 6OU A 708 " pdb=" O18 6OU A 708 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 4428 4.32 - 8.64: 49 8.64 - 12.97: 11 12.97 - 17.29: 0 17.29 - 21.61: 2 Bond angle restraints: 4490 Sorted by residual: angle pdb=" C PRO A 554 " pdb=" CA PRO A 554 " pdb=" CB PRO A 554 " ideal model delta sigma weight residual 111.56 93.15 18.41 1.65e+00 3.67e-01 1.25e+02 angle pdb=" N PRO A 554 " pdb=" CA PRO A 554 " pdb=" C PRO A 554 " ideal model delta sigma weight residual 112.47 134.08 -21.61 2.06e+00 2.36e-01 1.10e+02 angle pdb=" N CYS A 620 " pdb=" CA CYS A 620 " pdb=" C CYS A 620 " ideal model delta sigma weight residual 111.28 122.36 -11.08 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N ASP A 533 " pdb=" CA ASP A 533 " pdb=" C ASP A 533 " ideal model delta sigma weight residual 111.40 123.30 -11.90 1.22e+00 6.72e-01 9.52e+01 angle pdb=" N ILE A 339 " pdb=" CA ILE A 339 " pdb=" C ILE A 339 " ideal model delta sigma weight residual 110.62 117.70 -7.08 1.02e+00 9.61e-01 4.82e+01 ... (remaining 4485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.69: 1825 31.69 - 63.37: 41 63.37 - 95.06: 2 95.06 - 126.74: 3 126.74 - 158.43: 1 Dihedral angle restraints: 1872 sinusoidal: 725 harmonic: 1147 Sorted by residual: dihedral pdb=" C PRO A 554 " pdb=" N PRO A 554 " pdb=" CA PRO A 554 " pdb=" CB PRO A 554 " ideal model delta harmonic sigma weight residual -120.70 -106.85 -13.85 0 2.50e+00 1.60e-01 3.07e+01 dihedral pdb=" C15 6OU A 705 " pdb=" C16 6OU A 705 " pdb=" O18 6OU A 705 " pdb=" C19 6OU A 705 " ideal model delta sinusoidal sigma weight residual 175.68 -25.89 -158.43 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C07 6OU A 707 " pdb=" C08 6OU A 707 " pdb=" C09 6OU A 707 " pdb=" C10 6OU A 707 " ideal model delta sinusoidal sigma weight residual 179.90 -62.63 -117.47 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 1869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 417 0.085 - 0.171: 54 0.171 - 0.256: 14 0.256 - 0.341: 7 0.341 - 0.427: 2 Chirality restraints: 494 Sorted by residual: chirality pdb=" CA PRO A 554 " pdb=" N PRO A 554 " pdb=" C PRO A 554 " pdb=" CB PRO A 554 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CA HIS A 504 " pdb=" N HIS A 504 " pdb=" C HIS A 504 " pdb=" CB HIS A 504 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA PHE A 610 " pdb=" N PHE A 610 " pdb=" C PHE A 610 " pdb=" CB PHE A 610 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 491 not shown) Planarity restraints: 536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 597 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 598 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 598 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 598 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 266 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 267 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 503 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.56e+00 pdb=" C GLY A 503 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY A 503 " -0.008 2.00e-02 2.50e+03 pdb=" N HIS A 504 " -0.007 2.00e-02 2.50e+03 ... (remaining 533 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 1709 2.93 - 3.42: 3474 3.42 - 3.92: 5053 3.92 - 4.41: 5948 4.41 - 4.90: 8714 Nonbonded interactions: 24898 Sorted by model distance: nonbonded pdb=" O GLY A 286 " pdb=" OG1 THR A 289 " model vdw 2.438 3.040 nonbonded pdb=" O ILE A 271 " pdb=" OH TYR A 352 " model vdw 2.535 3.040 nonbonded pdb=" N TYR A 445 " pdb=" N GLY A 446 " model vdw 2.542 2.560 nonbonded pdb=" N GLY A 621 " pdb=" O GLY A 621 " model vdw 2.546 2.496 nonbonded pdb=" O LEU A 332 " pdb=" N PHE A 335 " model vdw 2.550 3.120 ... (remaining 24893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.420 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 3313 Z= 0.502 Angle : 1.268 21.609 4492 Z= 0.851 Chirality : 0.074 0.427 494 Planarity : 0.005 0.047 536 Dihedral : 14.325 158.427 1129 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.53 % Allowed : 7.28 % Favored : 90.19 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.40), residues: 384 helix: -0.06 (0.29), residues: 291 sheet: None (None), residues: 0 loop : -3.29 (0.53), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 624 TYR 0.011 0.001 TYR A 558 PHE 0.010 0.001 PHE A 609 TRP 0.005 0.001 TRP A 373 HIS 0.002 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00740 ( 3312) covalent geometry : angle 1.26851 ( 4490) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.12513 ( 2) hydrogen bonds : bond 0.24117 ( 213) hydrogen bonds : angle 8.06105 ( 621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: A 289 THR cc_start: 0.9175 (p) cc_final: 0.8894 (m) REVERT: A 377 LEU cc_start: 0.8440 (tp) cc_final: 0.7873 (mm) REVERT: A 399 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: A 400 LEU cc_start: 0.8060 (tp) cc_final: 0.7729 (mt) REVERT: A 427 LYS cc_start: 0.6832 (mptt) cc_final: 0.5924 (tttm) REVERT: A 550 GLU cc_start: 0.7439 (pm20) cc_final: 0.7206 (pm20) REVERT: A 569 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8388 (mm) REVERT: A 573 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.7010 (p90) outliers start: 8 outliers final: 3 residues processed: 114 average time/residue: 0.0653 time to fit residues: 8.9094 Evaluate side-chains 79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 573 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.147685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129623 restraints weight = 6103.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.132774 restraints weight = 3178.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134904 restraints weight = 2048.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136173 restraints weight = 1510.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.137212 restraints weight = 1235.314| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3313 Z= 0.177 Angle : 0.651 7.221 4492 Z= 0.354 Chirality : 0.040 0.150 494 Planarity : 0.005 0.044 536 Dihedral : 12.185 100.495 490 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.11 % Allowed : 13.29 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.41), residues: 384 helix: 1.71 (0.29), residues: 296 sheet: None (None), residues: 0 loop : -3.19 (0.53), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.016 0.002 TYR A 483 PHE 0.025 0.002 PHE A 596 TRP 0.012 0.001 TRP A 292 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3312) covalent geometry : angle 0.65076 ( 4490) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.46886 ( 2) hydrogen bonds : bond 0.07209 ( 213) hydrogen bonds : angle 5.06085 ( 621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.085 Fit side-chains REVERT: A 425 GLU cc_start: 0.6655 (mp0) cc_final: 0.6367 (mp0) REVERT: A 427 LYS cc_start: 0.6510 (mptt) cc_final: 0.5631 (tttm) REVERT: A 528 TRP cc_start: 0.9107 (t-100) cc_final: 0.8530 (t-100) REVERT: A 569 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7961 (mm) REVERT: A 573 TRP cc_start: 0.7500 (OUTLIER) cc_final: 0.7232 (p90) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.0420 time to fit residues: 4.6729 Evaluate side-chains 67 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 573 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.0470 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.149318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.130299 restraints weight = 6064.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133604 restraints weight = 3264.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.135868 restraints weight = 2135.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137186 restraints weight = 1585.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138324 restraints weight = 1301.871| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.137 Angle : 0.559 6.394 4492 Z= 0.300 Chirality : 0.039 0.177 494 Planarity : 0.004 0.040 536 Dihedral : 10.163 79.051 489 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.43 % Allowed : 17.09 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.43), residues: 384 helix: 2.09 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -3.33 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 548 TYR 0.011 0.001 TYR A 558 PHE 0.043 0.002 PHE A 596 TRP 0.015 0.001 TRP A 292 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3312) covalent geometry : angle 0.55942 ( 4490) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.13974 ( 2) hydrogen bonds : bond 0.05403 ( 213) hydrogen bonds : angle 4.33811 ( 621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.121 Fit side-chains REVERT: A 364 LYS cc_start: 0.7450 (ttpp) cc_final: 0.7153 (ttpt) REVERT: A 388 LYS cc_start: 0.7819 (mptt) cc_final: 0.7562 (mmtm) REVERT: A 399 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: A 425 GLU cc_start: 0.6787 (mp0) cc_final: 0.6541 (mp0) REVERT: A 427 LYS cc_start: 0.6417 (mptt) cc_final: 0.5530 (tttm) REVERT: A 528 TRP cc_start: 0.8979 (t-100) cc_final: 0.8697 (t-100) REVERT: A 577 ILE cc_start: 0.9121 (tp) cc_final: 0.8860 (tp) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.0526 time to fit residues: 5.7358 Evaluate side-chains 73 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN A 608 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124723 restraints weight = 6178.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.127811 restraints weight = 3461.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129913 restraints weight = 2327.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.131212 restraints weight = 1760.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132296 restraints weight = 1460.929| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3313 Z= 0.189 Angle : 0.608 7.600 4492 Z= 0.329 Chirality : 0.041 0.199 494 Planarity : 0.004 0.042 536 Dihedral : 8.852 60.142 485 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 6.01 % Allowed : 15.82 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.43), residues: 384 helix: 1.97 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -3.22 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 548 TYR 0.011 0.002 TYR A 558 PHE 0.054 0.002 PHE A 596 TRP 0.013 0.002 TRP A 514 HIS 0.006 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 3312) covalent geometry : angle 0.60831 ( 4490) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.19804 ( 2) hydrogen bonds : bond 0.06301 ( 213) hydrogen bonds : angle 4.67688 ( 621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.125 Fit side-chains REVERT: A 364 LYS cc_start: 0.7601 (ttpp) cc_final: 0.7277 (ttpt) REVERT: A 388 LYS cc_start: 0.7876 (mptt) cc_final: 0.7631 (mmtm) REVERT: A 569 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8114 (mm) outliers start: 19 outliers final: 16 residues processed: 73 average time/residue: 0.0538 time to fit residues: 5.0515 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 582 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.145467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126611 restraints weight = 6156.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129741 restraints weight = 3406.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131903 restraints weight = 2271.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133204 restraints weight = 1708.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134308 restraints weight = 1414.107| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3313 Z= 0.147 Angle : 0.559 6.492 4492 Z= 0.304 Chirality : 0.038 0.167 494 Planarity : 0.004 0.040 536 Dihedral : 7.994 58.280 485 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 6.01 % Allowed : 16.46 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.43), residues: 384 helix: 2.02 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -3.20 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.008 0.001 TYR A 558 PHE 0.019 0.001 PHE A 596 TRP 0.007 0.001 TRP A 373 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3312) covalent geometry : angle 0.55916 ( 4490) SS BOND : bond 0.00026 ( 1) SS BOND : angle 0.29295 ( 2) hydrogen bonds : bond 0.05592 ( 213) hydrogen bonds : angle 4.46968 ( 621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.121 Fit side-chains REVERT: A 364 LYS cc_start: 0.7602 (ttpp) cc_final: 0.7277 (ttpt) REVERT: A 388 LYS cc_start: 0.7856 (mptt) cc_final: 0.7654 (mmtm) REVERT: A 399 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7366 (mp-120) REVERT: A 569 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 577 ILE cc_start: 0.9119 (tp) cc_final: 0.8900 (tp) outliers start: 19 outliers final: 14 residues processed: 80 average time/residue: 0.0518 time to fit residues: 5.3066 Evaluate side-chains 78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 590 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.147133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128096 restraints weight = 6167.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131263 restraints weight = 3439.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133433 restraints weight = 2315.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.134716 restraints weight = 1751.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135847 restraints weight = 1455.515| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.134 Angle : 0.537 6.112 4492 Z= 0.289 Chirality : 0.038 0.171 494 Planarity : 0.004 0.039 536 Dihedral : 7.693 58.504 485 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 6.01 % Allowed : 17.09 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.44), residues: 384 helix: 2.08 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -3.28 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.009 0.001 TYR A 558 PHE 0.044 0.002 PHE A 596 TRP 0.007 0.001 TRP A 373 HIS 0.004 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 3312) covalent geometry : angle 0.53739 ( 4490) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.42597 ( 2) hydrogen bonds : bond 0.05222 ( 213) hydrogen bonds : angle 4.29091 ( 621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.127 Fit side-chains REVERT: A 335 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7489 (t80) REVERT: A 364 LYS cc_start: 0.7573 (ttpp) cc_final: 0.7265 (ttpt) REVERT: A 399 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: A 569 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 577 ILE cc_start: 0.9126 (tp) cc_final: 0.8891 (tp) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.0524 time to fit residues: 5.4653 Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126617 restraints weight = 6268.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129739 restraints weight = 3417.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131659 restraints weight = 2263.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133179 restraints weight = 1721.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134060 restraints weight = 1403.201| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.138 Angle : 0.554 8.404 4492 Z= 0.298 Chirality : 0.038 0.162 494 Planarity : 0.004 0.039 536 Dihedral : 7.747 59.668 485 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.33 % Allowed : 18.67 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.43), residues: 384 helix: 2.10 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.16 (0.54), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 548 TYR 0.008 0.001 TYR A 558 PHE 0.017 0.001 PHE A 596 TRP 0.013 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3312) covalent geometry : angle 0.55410 ( 4490) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.25298 ( 2) hydrogen bonds : bond 0.05146 ( 213) hydrogen bonds : angle 4.28699 ( 621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.130 Fit side-chains REVERT: A 335 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7521 (t80) REVERT: A 364 LYS cc_start: 0.7597 (ttpp) cc_final: 0.7276 (ttpt) REVERT: A 399 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: A 569 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8064 (mm) REVERT: A 577 ILE cc_start: 0.9151 (tp) cc_final: 0.8918 (tp) outliers start: 20 outliers final: 16 residues processed: 79 average time/residue: 0.0620 time to fit residues: 6.0599 Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 474 PHE Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.148305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129069 restraints weight = 6369.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132218 restraints weight = 3578.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134352 restraints weight = 2422.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135799 restraints weight = 1844.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136691 restraints weight = 1520.820| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.123 Angle : 0.528 8.203 4492 Z= 0.282 Chirality : 0.037 0.161 494 Planarity : 0.004 0.039 536 Dihedral : 7.208 57.257 485 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 6.01 % Allowed : 19.30 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.44), residues: 384 helix: 2.12 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.28 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 603 TYR 0.008 0.001 TYR A 558 PHE 0.053 0.002 PHE A 596 TRP 0.011 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3312) covalent geometry : angle 0.52851 ( 4490) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.26699 ( 2) hydrogen bonds : bond 0.04746 ( 213) hydrogen bonds : angle 4.13756 ( 621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.115 Fit side-chains REVERT: A 335 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7587 (t80) REVERT: A 364 LYS cc_start: 0.7579 (ttpp) cc_final: 0.7263 (ttpt) REVERT: A 399 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: A 569 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8105 (mm) REVERT: A 577 ILE cc_start: 0.9084 (tp) cc_final: 0.8876 (tp) outliers start: 19 outliers final: 14 residues processed: 77 average time/residue: 0.0575 time to fit residues: 5.5405 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.0170 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.146028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127065 restraints weight = 6306.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130209 restraints weight = 3446.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132329 restraints weight = 2278.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133667 restraints weight = 1703.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134739 restraints weight = 1406.119| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3313 Z= 0.133 Angle : 0.545 8.611 4492 Z= 0.294 Chirality : 0.038 0.158 494 Planarity : 0.004 0.039 536 Dihedral : 7.102 58.156 485 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.38 % Allowed : 19.62 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.44), residues: 384 helix: 2.06 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.22 (0.53), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 570 TYR 0.008 0.001 TYR A 558 PHE 0.020 0.001 PHE A 596 TRP 0.009 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 3312) covalent geometry : angle 0.54498 ( 4490) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.22323 ( 2) hydrogen bonds : bond 0.04870 ( 213) hydrogen bonds : angle 4.22270 ( 621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.112 Fit side-chains REVERT: A 332 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8235 (tt) REVERT: A 335 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7616 (t80) REVERT: A 364 LYS cc_start: 0.7607 (ttpp) cc_final: 0.7296 (ttpt) REVERT: A 399 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7227 (mp-120) REVERT: A 569 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 577 ILE cc_start: 0.9121 (tp) cc_final: 0.8895 (tp) outliers start: 17 outliers final: 13 residues processed: 74 average time/residue: 0.0644 time to fit residues: 5.9112 Evaluate side-chains 76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.144173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125230 restraints weight = 6232.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.128270 restraints weight = 3415.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130388 restraints weight = 2275.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131681 restraints weight = 1713.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132779 restraints weight = 1418.760| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.140 Angle : 0.565 8.461 4492 Z= 0.302 Chirality : 0.038 0.166 494 Planarity : 0.004 0.039 536 Dihedral : 7.019 58.883 485 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.70 % Allowed : 19.94 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.43), residues: 384 helix: 2.04 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.18 (0.53), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 548 TYR 0.008 0.001 TYR A 558 PHE 0.050 0.002 PHE A 596 TRP 0.009 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3312) covalent geometry : angle 0.56464 ( 4490) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.17415 ( 2) hydrogen bonds : bond 0.04992 ( 213) hydrogen bonds : angle 4.17372 ( 621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.155 Fit side-chains REVERT: A 332 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8220 (tt) REVERT: A 335 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7656 (t80) REVERT: A 364 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7323 (ttpt) REVERT: A 569 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8173 (mm) REVERT: A 577 ILE cc_start: 0.9076 (tp) cc_final: 0.8864 (tp) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.0612 time to fit residues: 5.6406 Evaluate side-chains 80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 445 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126118 restraints weight = 6213.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129222 restraints weight = 3362.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131389 restraints weight = 2207.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.132691 restraints weight = 1642.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133374 restraints weight = 1352.609| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3313 Z= 0.134 Angle : 0.574 8.135 4492 Z= 0.307 Chirality : 0.038 0.149 494 Planarity : 0.004 0.039 536 Dihedral : 6.989 59.802 485 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.38 % Allowed : 20.57 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.43), residues: 384 helix: 2.03 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -3.15 (0.52), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.008 0.001 TYR A 558 PHE 0.020 0.001 PHE A 596 TRP 0.008 0.001 TRP A 573 HIS 0.003 0.001 HIS A 616 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3312) covalent geometry : angle 0.57402 ( 4490) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.21122 ( 2) hydrogen bonds : bond 0.04871 ( 213) hydrogen bonds : angle 4.20678 ( 621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 749.16 seconds wall clock time: 13 minutes 30.63 seconds (810.63 seconds total)